Linux CLI manual and file streaming
an-altosian opened this issue · comments
Dear DiaNN authors,
Thank you very much for developing such a nice tool.
I am trying to run DIA-NN from a linux server using your CLI. I noticed that there is no helping messages, i.e., --help flag, describing the available parameters and the default values. This makes it slightly difficult to setup a pipeline that can take parameter values as the inputs as I found some descrepancy between the log.txt file and the parameters listed in the log.txt file, for example the --qvalue and --min-corr parameters are not listed in the README. So, do you think it is possible to provide a command line manual that refects the up-to-date parameters?
Another question is, as the current linux version of DIANN could not process .RAW files, I have to convert my files first to mxML, which can take enormous disk space. As a workaround, do you think it is possible for DIANN CLI to take a file stream as an alternative of its --f parameter?
Best.
Thank you for pointing this out, indeed seems some parameters are missing in the command line reference.
About mzML: it's usually OK size-wise, if you use 32-bit format, i.e. please see the recommended conversion settings: https://github.com/vdemichev/DiaNN?tab=readme-ov-file#raw-data-formats.
About a stream: not sure, most likely not. What's planned though is native .raw support under Linux.
Best,
Vadim
Thanks for the answers! Could I ask when would you expect the native .raw support to be released?
Best
No definitive timeline for this yet, but almost definitely not in the upcoming update (1.9.1).
Cool! Then I will focus on data conversion for now. Thanks for the prompt replies!